A vast number of new drug targets are now being identified using a combination of genomics, bioinformatics, genetics, and high-throughput (HTP) biochemistry. Genomics provides information on the genetic composition and the activity of an organism""s genes. Bioinformatics uses computer algorithms to recognize and predict structural patterns in DNA and proteins, defining families of related genes and proteins. The information gained from the combination of these approaches is expected to boost the number of drug targets, usually proteins, from the current 500 to over 10,000 in the coming decade.
The number of chemical compounds available for screening as potential drugs is also growing dramatically due to recent advances in combinatorial chemistry, the production of large numbers of organic compounds through rapid parallel and automated synthesis. The compounds produced in the combinatorial libraries being generated will far outnumber those compounds being prepared by traditional, manual means, natural product extracts, or those in the historical compound files of large pharmaceutical companies.
Both the rapid increase of new drug targets and the availability of vast libraries of chemical compounds creates an enormous demand for new technologies which improve the screening process. Current technological approaches which attempt to address this need include multiwell-plate based screening systems, cell-based screening systems, microfluidics-based screening systems, and screening of soluble targets against solid-phase synthesized drug components.
Automated multiwell formats are the best developed high-throughput screening systems. Automated 96-well plate-based screening systems are the most widely used. The current trend in plate based screening systems is to reduce the volume of the reaction wells further, thereby increasing the density of the wells per plate (96-well to 384-, and 1536-well per plate). The reduction in reaction volumes results in increased throughput, dramatically decreased bioreagent costs, and a decrease in the number of plates which need to be managed by automation.
However, although increases in well numbers per plate are desirable for high throughput efficiency, the use of volumes smaller than 1 microliter in the well format generates significant problems with evaporation, dispensing times, protein inactivation, and assay adaptation. Proteins are very sensitive to the physical and chemical properties of the reaction chamber surfaces. Proteins are prone to denaturation at the liquid/solid and liquid/air interfaces. Miniaturization of assays to volumes smaller than 1 microliter increases the surface to volume ratio substantially. (Changing volumes from 1 microliter to 10 nanoliter increases the surface ratio by 460%, leading to increased protein inactivation.) Furthermore, solutions of submicroliter volumes evaporate rapidly, within seconds to a few minutes, when in contact with air. Maintaining microscopic volumes in open systems is therefore very difficult.
Other types of high-throughput assays, such as miniaturized cell-based assays are also being developed. Miniaturized cell-based assays have the potential to generate screening data of superior quality and accuracy, due to their in vivo nature. However, the interaction of drug compounds with proteins other than the desired targets is a serious problem related to this approach which leads to a high rate of false positive results.
Microfluidics-based screening systems that measure in vitro reactions in solution make use of ten to several-hundred micrometer wide channels. Micropumps, electroosmotic flow, integrated valves and mixing devices control liquid movement through the channel network. Microfluidic networks prevent evaporation but, due to the large surface to volume ratio, result in significant protein inactivation. The successful use of microfluidic networks in biomolecule screening remains to be shown.
Drug screening of soluble targets against solid-phase synthesized drug components is intrinsically limited. The surfaces required for solid state organic synthesis are chemically diverse and often cause the inactivation or non-specific binding of proteins, leading to a high rate of false-positive results. Furthermore, the chemical diversity of drug compounds is limited by the combinatorial synthesis approach that is used to generate the compounds at the interface. Another major disadvantage of this approach stems from the limited accessibility of the binding site of the soluble target protein to the immobilized drug candidates.
DNA microarray technology is not immediately transferable to protein screening microdevices. To date, microarrays are exclusively available for nucleic acid hybridization assays (xe2x80x98DNA-chipsxe2x80x99). Their underlying chemistry and materials are not readily transferable to protein assays. Nucleic acids withstand temperatures up to 100xc2x0 C., can be dried and re-hydrated without loss of activity and bound directly to organic adhesion layers absorbed on surfaces such as glass. In contrast, proteins must remain hydrated, kept at ambient temperatures, and are very sensitive to the physical and chemical properties of the support materials. Therefore, maintaining protein activity at the liquid-solid interface requires entirely different immobilization strategies than those used for nucleic acids. Additionally, the proper orientation of the protein at the interface is desirable to ensure accessibility of their active sites with interacting molecules.
In addition to the goal of achieving high-throughput screening of compounds against targets to identify potential drug leads, researchers also need to be able to identify a highly specific lead compound early in the drug discovery process. Analyzing a multitude of members of a protein family or forms of a polymorphic protein in parallel enables quick identification of highly specific lead compounds. Proteins within a structural family share similar binding sites and catalytic mechanisms. Often, a compound that effectively interferes with the activity of one family member also interferes with other members of the same family. Using standard technology to discover such additional interactions requires a tremendous effort in time and costs and as a consequence is simply not done.
However, cross-reactivity of a drug with related proteins can be the cause of low efficacy or even side effects in patients. For instance, AZT, a major treatment for AIDS, blocks not only viral polymerases, but also human polymerases, causing deleterious side effects. Cross-reactivity with closely related proteins is also a problem with nonsteroidal anti-inflammatory drugs (NSAIDs) and aspirin. These drugs inhibit cyclooxygenase-2, an enzyme which promotes pain and inflammation. However, the same drugs also strongly inhibit a related enzyme, cyclooxygenase-1, that is responsible for keeping the stomach lining and kidneys healthy, leading to common side-effects including stomach irritation.
For the foregoing reasons, there is a need for miniaturized protein arrays and for methods for the parallel, in vitro, high-throughput screening of functionally and/or structurally related protein targets against potential drug compounds in a manner that minimizes reagent volumes and protein inactivation problems.
The present invention is directed to protein arrays, protein-coated substrates, and methods of use thereof that satisfy the need for parallel, in vitro, high-throughput screening of functionally or structurally related protein targets against potential drug compounds in a manner that minimizes reagent volumes and protein inactivation problems.
In one embodiment, the present invention provides for a protein-coated substrate comprising a plurality of patches arranged in discrete, known regions on a substrate, where a protein with a different, known sequence is immobilized on each patch. Furthermore, each of the patches of the protein-coated substrate of the present invention is separated from neighboring patches by from about 50 nm to about 500 xcexcm.
Biosensors, micromachined devices, and medical devices that comprise the protein-coated substrate of the present invention represent other aspects of the invention.
The present invention also provides an array of proteins comprising a plurality of patches arranged in discrete, known regions on a substrate, where a protein with a different, known sequence is immobilized on each patch. Furthermore, each of the patches of the protein-coated substrate of the present invention is separated from neighboring patches by from about 50 nm to about 500 xcexcm.
The protein immobilized on one patch of the array is preferably different from the protein immobilized on a second patch. In an especially preferred embodiment, the protein that is immobilized on one patch of the array is a member of the same protein family as or is otherwise functionally or structurally related to the proteins immobilized on the other patches of the array.
The patches of the array may also optionally further comprise monolayers (on which the proteins of the patches are immobilized).
At least one coating may be formed on the substrate or applied to the substrate of an array of the present invention such that the coating is positioned between the substrate and the monolayer of each patch.
The coating, or the substrate itself if no coating is used, may optionally possess an ultraflat surface with a mean roughness of less than about 5 angstroms for areas of at least 25 xcexcm2. This ultraflat surface optionally may be produced by template stripping.
The monolayer of a patch on the array of the present invention may be a mixed monolayer composed of more than one type of molecule.
The patches of an array of the present invention may further comprise an affinity tag that enhances site-specific immobilization of the biological moiety onto the monolayer.
In one embodiment of the invention, an adaptor molecule may also be present to link the affinity tag to the biological moiety on the patches of the array.
In another version of the invention, the affinity tag, biological moiety, and the adaptor (if present) preferably constitute a fusion protein.
The present invention further provides for methods of using the array to screen a plurality of proteins in parallel for their ability to bind or otherwise interact with a component of a fluid sample. Most of these methods involve first delivering the fluid sample to the array. If binding is to be detected, the array may then be optionally washed to remove any unbound component from the area. The methods then involve detecting, either directly or indirectly, the presence or absence of the component retained at each patch or other evidence of an interaction of the protein of a given patch with the component.
Similar methods may be used diagnostically to screen a fluid sample with the array for the presence, absence, or amount of a plurality of analytes at the same time.
The present invention also provides for methods of determining in parallel whether or not a plurality of proteins belongs to a certain protein family. These methods involve delivering a fluid sample comprising a ligand of a known protein family to the patches of the array and then detecting, either directly or indirectly, for the interaction or binding of the known ligand to the patches that would be characteristic the known protein family.
Another aspect of the invention is a protein-coated substrate that comprises a fusion protein immobilized on a monolayer on a portion of the surface of a substrate. The fusion protein is immobilized with the aid of an affinity tag that enhances the site-specific immobilization of the fusion protein onto the monolayer. Here the fusion protein comprises a polypeptide that serves as an adaptor molecule by linking another polypeptide to the affinity tag. The monolayer of the protein-coated substrate comprises molecules of the formula X-R-Y where R is a spacer, X is a functional group that binds R to the surface, and Y is a functional group for binding the fusion protein onto the monolayer. The protein-coated substrate may optionally also include a coating between the substrate and the monolayer and the affinity tag may optionally constitute a part of the fusion protein.